[2023-06-18 13:18:42,073] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:18:42,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:18:42,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference
[2023-06-18 13:18:44,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:18:44,423] [INFO] Task started: Prodigal
[2023-06-18 13:18:44,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgd785911b-92e0-4729-9147-5cbd1ee33991/GCA_018653165.1_ASM1865316v1_genomic.fna.gz | prodigal -d GCA_018653165.1_ASM1865316v1_genomic.fna/cds.fna -a GCA_018653165.1_ASM1865316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:18:56,225] [INFO] Task succeeded: Prodigal
[2023-06-18 13:18:56,226] [INFO] Task started: HMMsearch
[2023-06-18 13:18:56,226] [INFO] Running command: hmmsearch --tblout GCA_018653165.1_ASM1865316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/reference_markers.hmm GCA_018653165.1_ASM1865316v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:18:56,498] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:18:56,499] [INFO] Found 6/6 markers.
[2023-06-18 13:18:56,551] [INFO] Query marker FASTA was written to GCA_018653165.1_ASM1865316v1_genomic.fna/markers.fasta
[2023-06-18 13:18:56,552] [INFO] Task started: Blastn
[2023-06-18 13:18:56,552] [INFO] Running command: blastn -query GCA_018653165.1_ASM1865316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/reference_markers.fasta -out GCA_018653165.1_ASM1865316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:18:57,206] [INFO] Task succeeded: Blastn
[2023-06-18 13:18:57,213] [INFO] Selected 31 target genomes.
[2023-06-18 13:18:57,214] [INFO] Target genome list was writen to GCA_018653165.1_ASM1865316v1_genomic.fna/target_genomes.txt
[2023-06-18 13:18:57,219] [INFO] Task started: fastANI
[2023-06-18 13:18:57,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgd785911b-92e0-4729-9147-5cbd1ee33991/GCA_018653165.1_ASM1865316v1_genomic.fna.gz --refList GCA_018653165.1_ASM1865316v1_genomic.fna/target_genomes.txt --output GCA_018653165.1_ASM1865316v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:19:15,998] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:15,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:19:16,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:19:16,002] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:19:16,002] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:19:16,003] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-18 13:19:16,006] [INFO] DFAST Taxonomy check result was written to GCA_018653165.1_ASM1865316v1_genomic.fna/tc_result.tsv
[2023-06-18 13:19:16,007] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:19:16,007] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:19:16,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/checkm_data
[2023-06-18 13:19:16,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:19:16,062] [INFO] Task started: CheckM
[2023-06-18 13:19:16,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018653165.1_ASM1865316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018653165.1_ASM1865316v1_genomic.fna/checkm_input GCA_018653165.1_ASM1865316v1_genomic.fna/checkm_result
[2023-06-18 13:19:55,330] [INFO] Task succeeded: CheckM
[2023-06-18 13:19:55,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:19:55,368] [INFO] ===== Completeness check finished =====
[2023-06-18 13:19:55,368] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:19:55,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018653165.1_ASM1865316v1_genomic.fna/markers.fasta)
[2023-06-18 13:19:55,369] [INFO] Task started: Blastn
[2023-06-18 13:19:55,369] [INFO] Running command: blastn -query GCA_018653165.1_ASM1865316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b631634-cbcc-42a6-9aad-5229db37c587/dqc_reference/reference_markers_gtdb.fasta -out GCA_018653165.1_ASM1865316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:56,358] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:56,363] [INFO] Selected 14 target genomes.
[2023-06-18 13:19:56,363] [INFO] Target genome list was writen to GCA_018653165.1_ASM1865316v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:19:56,369] [INFO] Task started: fastANI
[2023-06-18 13:19:56,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgd785911b-92e0-4729-9147-5cbd1ee33991/GCA_018653165.1_ASM1865316v1_genomic.fna.gz --refList GCA_018653165.1_ASM1865316v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018653165.1_ASM1865316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:20:05,833] [INFO] Task succeeded: fastANI
[2023-06-18 13:20:05,842] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:20:05,843] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018665025.1	s__UBA9659 sp018665025	99.4385	1174	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	conclusive
GCA_012961165.1	s__UBA9659 sp012961165	94.5404	1082	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018645845.1	s__UBA9659 sp018645845	89.1738	778	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
GCA_018667205.1	s__UBA9659 sp018667205	83.3189	542	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607685.1	s__UBA9659 sp018607685	81.6022	585	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642855.1	s__UBA9659 sp017642855	75.746	81	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
GCA_016779585.1	s__UBA9659 sp016779585	75.4962	77	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:20:05,846] [INFO] GTDB search result was written to GCA_018653165.1_ASM1865316v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:20:05,847] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:20:05,851] [INFO] DFAST_QC result json was written to GCA_018653165.1_ASM1865316v1_genomic.fna/dqc_result.json
[2023-06-18 13:20:05,852] [INFO] DFAST_QC completed!
[2023-06-18 13:20:05,852] [INFO] Total running time: 0h1m24s